DFT Investigation of the Electronic Structure, Non-Covalent Interactions, and Muon Hyperfine Interactions in Short...

Muonium (Mu) trapping sites and the associated hyperfine interactions in 1, 2, 3, and 4 base-pair adenine-thymine double-strand DNA molecules were investigated using the density functional theory method. Based on relative energy analysis, C8-A is the lowest energy Mu site in the 1, 2, and 3 base-pair molecules. In the 4 base-pair molecule, N3-A has the lowest energy while C8-A sites are ranked fifth and above. The muon hyperfine coupling constant at N3-A is however very small. Visual analysis of the unpaired spin distribution shows that at N3-A, Mu sits at a position where no significant spin density is localized. Noncovalent interaction (NCI) analysis based on the reduced density gradient revealed that the hydrogen bond is a significant factor in stabilizing the Mu sites. The NCI isosurface plot demonstrates that van der Waals attraction also plays a role in the interaction between Mu and its surroundings. The scatter plot of the predicted ALC-μSR spectrum indicates that there are overlaps of polarization dips in the 3 base-pair molecule. No such overlaps are found for the 4 base-pair molecule. The 1 and 2 base-pair nonmuoniated molecules have a similar HOMO-LUMO gap (4.498 and 4.556 eV). The HOMO-LUMO gap reduces significantly as the number of base pairs increases to three and four (3.922 and 3.952 eV).